There are two hidden rooms; one behind the altar and another on the left wall while descending the stairs from the altar. They are unlocked after completing certain quests:

The hidden wall behind the altar is revealed after completing The Blood of Bafalgar. It will lead to a corridor and at the end of the corridor where a quest item, the Ancient Lily, can be found. It is required for quest A Flower for a Rose.

The hidden wall on the left side of the wall (after descending the stairs) is revealed after completing The Coffin of Bafalgar. Enter the room to find another Secret Area, Soothsayer's Crypt.